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Dragen bio it platform germline pipeline

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The DRAGEN Bio-IT Platform Germline Pipeline is a hardware-accelerated bioinformatics solution designed for rapid and accurate analysis of whole-genome, whole-exome, and targeted DNA sequencing data. The platform provides highly optimized algorithms for key steps in the germline analysis workflow, including read alignment, variant calling, and annotation.

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DRAGEN Bio-IT Platform (29 citations) DRAGEN (13 citations) DRAGEN pipeline (9 citations) DRAGEN Bio-IT (8 citations) DRAGEN Bio-IT Platform Germline Pipeline v3.0.7 (7 citations) Illumina pipelines (6 citations) DRAGEN Germline Pipeline (5 citations) DRAGEN Platform (4 citations) Bio-IT Platform (3 citations) Germline Pipeline (2 citations)

3 protocols using dragen bio it platform germline pipeline

1

UK Biobank Exome Sequencing Pipeline

Cited 1 time
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The 302,355 UKB exome sequences were processed at AstraZeneca from their unaligned FASTQ state. A custom-built Amazon Web Services (AWS) cloud compute platform running Illumina DRAGEN Bio-IT Platform Germline Pipeline v3.0.7 was used to align the reads to the GRCh38 genome reference and perform single-nucleotide variant (SNV) and insertion and deletion (indel) calling. SNVs and indels were annotated using SnpEFF v4.348 (link) against Ensembl Build 38.9249 (link). We further annotated all variants with their genome Aggregation Database (gnomAD) MAFs (gnomAD v2.1.1 mapped to GRCh38)27 (link). We also annotated missense variants with MTR and REVEL scores35 (link),50 (link).
Wang Q., Dhindsa R.S., Carss K., Harper A.R., Nag A., Tachmazidou I., Vitsios D., Deevi S.V., Mackay A., Muthas D., Hühn M., Monkley S., Olsson H., Wasilewski S., Smith K.R., March R., Platt A., Haefliger C, & Petrovski S. (2021). Rare variant contribution to human disease in 281,104 UK Biobank exomes. Nature, 597(7877), 527-532.
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2

UKB Exome Sequencing Processing

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The 469,809 UKB exome sequences were processed at AstraZeneca from their unaligned FASTQ state. A custom-built Amazon Web Services (AWS) cloud computing platform running Illumina DRAGEN Bio-IT Platform Germline Pipeline v.3.0.7 was used to align the reads to the GRCh38 genome reference and to perform single-nucleotide variant (SNV) and insertion and deletion (indel) calling. SNVs and indels were annotated using SnpEFF v.4.3 (ref. 62 (link)) against Ensembl Build 38.92 (ref. 63 (link)). We further annotated all variants with their gnomAD MAFs (gnomAD v.2.1.1 mapped to GRCh38)64 (link). We also annotated missense variants with MTR and REVEL scores16 (link),29 (link). The AstraZeneca pipeline output files including the variant call format files are available through UKB Showcase (https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=172).
Dhindsa R.S., Burren O.S., Sun B.B., Prins B.P., Matelska D., Wheeler E., Mitchell J., Oerton E., Hristova V.A., Smith K.R., Carss K., Wasilewski S., Harper A.R., Paul D.S., Fabre M.A., Runz H., Viollet C., Challis B., Platt A., Vitsios D., Ashley E.A., Whelan C.D., Pangalos M.N., Wang Q, & Petrovski S. (2023). Rare variant associations with plasma protein levels in the UK Biobank. Nature, 622(7982), 339-347.
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3

UKB Exome Sequencing Processing

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The 469,809 UKB exome sequences were processed at AstraZeneca from their unaligned FASTQ state. A custom-built Amazon Web Services (AWS) cloud computing platform running Illumina DRAGEN Bio-IT Platform Germline Pipeline v.3.0.7 was used to align the reads to the GRCh38 genome reference and to perform single-nucleotide variant (SNV) and insertion and deletion (indel) calling. SNVs and indels were annotated using SnpEFF v.4.3 (ref. 62 (link)) against Ensembl Build 38.92 (ref. 63 (link)). We further annotated all variants with their gnomAD MAFs (gnomAD v.2.1.1 mapped to GRCh38)64 (link). We also annotated missense variants with MTR and REVEL scores16 (link),29 (link). The AstraZeneca pipeline output files including the variant call format files are available through UKB Showcase (https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=172).
Dhindsa R.S., Burren O.S., Sun B.B., Prins B.P., Matelska D., Wheeler E., Mitchell J., Oerton E., Hristova V.A., Smith K.R., Carss K., Wasilewski S., Harper A.R., Paul D.S., Fabre M.A., Runz H., Viollet C., Challis B., Platt A., Vitsios D., Ashley E.A., Whelan C.D., Pangalos M.N., Wang Q, & Petrovski S. (2023). Rare variant associations with plasma protein levels in the UK Biobank. Nature, 622(7982), 339-347.
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